Methods and compositions for determining responsiveness to treatment with a tnf-alpha inhibitor

Abstract

The present invention is directed to methods and compositions useful for predicting the efficacy of a TNFα inhibitor for treating an inflammatory bowel disease (IBD). The invention includes, in one embodiment, determining the level of expression of TNFα by delivering a labeled anti-TNFα antibody on to the cells of the intestinal mucosa of a subject having IBD, whereby the TNFα level of expression can be used to predict whether the subject will be responsive or not to the antibody therapy. Levels of TNFα may be determined in vivo or ex vivo. The invention further provides methods of locally administering a TNFα antibody, e.g., topically to the intestinal mucosa, for the treatment of IBD.

1 . A method for determining the responsiveness of a subject having inflammatory bowel disease (IBD) to treatment with a TNFα inhibitor, the method comprising
 determining the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD; and 
 comparing the level of expression of TNFα in the cells of the intestinal mucosa of the subject to a control level of expression of TNFα from a non-responder, 
 wherein a higher level of expression of TNFα in the cells of the intestinal mucosa of the subject as compared to the control level of expression of TNFα indicates that the subject will be responsive to treatment with the TNFα inhibitor, thereby predicting the responsiveness of the subject having IBD to treatment with the TNFα inhibitor. 
 
     
     
         2 . A method of determining whether a TNFα inhibitor will be effective for the treatment of a subject having inflammatory bowel disease (IBD), the method comprising
 determining the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD, 
 wherein a higher level of expression of TNFα in the cells of the intestinal mucosa of the subject as compared to a control level of expression of TNFα for a nonresponder indicates that the TNFα inhibitor will be effective for the treatment of the subject having IBD, thereby determining whether a TNFα inhibitor will be effective for the treatment of the subject having IBD. 
 
     
     
         3 . A method for treating a subject having inflammatory bowel disease (IBD), comprising
 determining the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD; and   administering a TNFα inhibitor to the subject having IBD, provided that the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD is higher than a control level of expression of TNFα for a nonresponder, thereby treating the subject having IBD.   
     
     
         4 . The method of any one of  claims 1 - 3 , wherein the IBD is Crohn's disease or ulcerative colitis. 
     
     
         5 . The method of any one of  claims 1 - 3 , wherein the level of expression of membrane TNFα (mTNFα) in the cells of the intestinal mucosa of the subject having IBD is determined. 
     
     
         6 . The method of any one of  claims 1 - 3 , wherein determining the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD comprises topically applying a detectably labeled TNFα inhibitor to the cells of the intestinal mucosa of the subject having IBD. 
     
     
         7 . The method of  claim 6 , wherein the detectably labeled TNFα inhibitor is topically applied to the cells of the intestinal mucosa of the subject having IBD during colonoscopy. 
     
     
         8 . The method of any one of  claims 1 - 3 , wherein the level of expression of TNFα is determined using an in vivo assay. 
     
     
         9 . The method of any one of  claims 1 - 3 , wherein the level of expression of TNFα is determined using an ex vivo assay. 
     
     
         10 . The method of  claim 9 , wherein the level of expression of TNFα in the sample is determined by a technique selected from the group consisting of immunohistochemistry, immunocytochemistry, flow cytometry, ELISA and mass spectrometry. 
     
     
         11 . The method of any one of  claims 1 - 3 , wherein the level of expression of TNFα in the sample is determined at the nucleic acid level. 
     
     
         12 . The method of  claim 11 , wherein the nucleic acid level is determined using either quantitative polymerase chain reaction or expression array analysis. 
     
     
         13 . The method of any one of  claims 1 - 3 , wherein the level of expression of TNFα is determined by confocal laser endomicroscopy. 
     
     
         14 . The method of any one of  claims 1 - 3 , wherein the TNFα inhibitor is an anti-TNFα antibody, or antigen-binding portion thereof. 
     
     
         15 . The method of  claim 14 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is selected from the group consisting of a human antibody, a chimeric antibody, and a humanized antibody. 
     
     
         16 . The method of  claim 15 , wherein the chimeric anti-TNFα antibody, or antigen-binding portion thereof, is infliximab. 
     
     
         17 . The method of  claim 15 , wherein the human anti-TNFα antibody, or antigen-binding portion thereof, is adalimumab or golimumab. 
     
     
         18 . The method of  claim 15 , wherein the human anti-TNFα antibody, or antigen-binding portion thereof, is selected from the group consisting of
 (a) an isolated human antibody that dissociates from human TNFα with a K d  of 1×10 −8  M or less and a k off  rate constant of 1×10 −3  s −1  or less, both determined by surface plasmon resonance, and neutralizes human TNFα cytotoxicity in a standard in vitro L929 assay with an IC 50  of 1×10 −7  M or less; 
 (b) an isolated human antibody comprising
 a light chain variable region comprising a CDR3 domain comprising the amino acid sequence of SEQ ID NO: 3, a CDR2 domain comprising the amino acid sequence of SEQ ID NO: 5, and a CDR1 domain comprising the amino acid sequence of SEQ ID NO: 7, and 
 a heavy chain variable region comprising a CDR3 domain comprising the amino acid sequence of SEQ ID NO: 4, a CDR2 domain comprising the amino acid sequence of SEQ ID NO: 6, and a CDR1 domain comprising the amino acid sequence of SEQ ID NO: 8, and 
 
 (c) an isolated human antibody comprising a light chain variable region (LCVR) comprising the amino acid sequence of SEQ ID NO: 1 and a heavy chain variable region (HCVR) comprising the amino acid sequence of SEQ ID NO: 2. 
 
     
     
         19 - 20 . (canceled) 
     
     
         21 . The method of any one of  claims 1 - 3 , wherein the method determines or predicts clinical responsiveness in the subject. 
     
     
         22 . A method for treating a subject having inflammatory bowel disease (IBD), the method comprising
 selecting a subject having IBD and having a level of expression of TNFα in the intestinal mucosa which is higher than a control level of expression of TNFα from a nonresponder; and   topically administering a TNFα inhibitor to the intestinal mucosa of the subject having IBD, thereby treating the subject having IBD.   
     
     
         23 . The method of  claim 22 , wherein the IBD is Crohn's disease or ulcerative colitis. 
     
     
         24 . The method of  claim 22 , wherein the TNFα inhibitor is administered using a spraying catheter. 
     
     
         25 . The method of  claim 22 , wherein the level of expression of membrane TNFα (mTNFα) in the cells of the intestinal mucosa of the subject having IBD is determined. 
     
     
         26 . The method of  claim 22 , wherein the level of expression of TNFα is determined using an in vivo assay or an ex vivo assay. 
     
     
         27 . The method of  claim 22 , wherein the TNFα inhibitor is an anti-TNFα antibody, or antigen-binding portion thereof. 
     
     
         28 . The method of  claim 27 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is selected from the group consisting of a human antibody, a chimeric antibody, and a humanized antibody. 
     
     
         29 . The method of  claim 28 , wherein the chimeric anti-TNFα antibody, or antigen-binding portion thereof, is infliximab. 
     
     
         30 . The method of  claim 28 , wherein the human anti-TNFα antibody, or antigen-binding portion thereof, is adalimumab or golimumab. 
     
     
         31 . The method of  claim 28 , wherein the human anti-TNFα antibody, or antigen-binding portion thereof, is
 (a) an isolated human antibody that dissociates from human TNFα with a K d  of 1×10 −8  M or less and a k off  rate constant of 1×10 −3  s −1  or less, both determined by surface plasmon resonance, and neutralizes human TNFα cytotoxicity in a standard in vitro L929 assay with an IC 50  of 1×10 −7  M or less; 
 (b) an isolated human antibody comprising
 a light chain variable region comprising a CDR3 domain comprising the amino acid sequence of SEQ ID NO: 3, a CDR2 domain comprising the amino acid sequence of SEQ ID NO: 5, and a CDR1 domain comprising the amino acid sequence of SEQ ID NO: 7, and 
 a heavy chain variable region comprising a CDR3 domain comprising the amino acid sequence of SEQ ID NO: 4, a CDR2 domain comprising the amino acid sequence of SEQ ID NO: 6, and a CDR1 domain comprising the amino acid sequence of SEQ ID NO: 8, and 
 (c) an isolated human antibody comprising a light chain variable region (LCVR) comprising the amino acid sequence of SEQ ID NO: 1 and a heavy chain variable region (HCVR) comprising the amino acid sequence of SEQ ID NO: 2. 
 
 
     
     
         32 - 33 . (canceled) 
     
     
         34 . A kit for determining if a TNFα inhibitor will be effective for the treatment of a subject having inflammatory bowel disease (IBD), the kit comprising
 a means for determining the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD, and 
 instructions for recommended treatment for the subject based on the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD, 
 wherein a higher level of expression of TNFα in the cells of the intestinal mucosa of the subject as compared to a control level of expression of TNFα from a nonresponder indicates that the TNFα inhibitor will be effective for the treatment of the subject having IBD. 
 
     
     
         35 . The kit of  claim 34 , further comprising a pharmaceutical composition comprising the TNFα inhibitor. 
     
     
         36 . The kit of  claim 34 , wherein the means for determining the level of expression of TNFα in the cells of the intestinal mucosa of the subject having IBD comprises a detectably labeled anti-TNFα antibody, or antigen-binding portion thereof. 
     
     
         37 . The kit of  claim 36 , wherein the detectably labeled anti-TNFα antibody, or antigen-binding portion thereof, is labeled with fluorescein isothiocyanate (FITC). 
     
     
         38 . The kit of  claim 36 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is infliximab. 
     
     
         39 . The kit of  claim 36 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is adalimumab or golimumab. 
     
     
         40 . The kit of  claim 36 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is
 (a) an isolated human antibody that dissociates from human TNFα with a K d  of 1×10 −8  M or less and a k off  rate constant of 1×10 −3  s −1  or less, both determined by surface plasmon resonance, and neutralizes human TNFα cytotoxicity in a standard in vitro L929 assay with an IC 50  of 1×10 −7  M or less; 
 (b) an isolated human antibody comprising
 a light chain variable region comprising a CDR3 domain comprising the amino acid sequence of SEQ ID NO: 3, a CDR2 domain comprising the amino acid sequence of SEQ ID NO: 5, and a CDR1 domain comprising the amino acid sequence of SEQ ID NO: 7, and a heavy chain variable region comprising a CDR3 domain comprising the amino acid sequence of SEQ ID NO: 4, a CDR2 domain comprising the amino acid sequence of SEQ ID NO: 6, and a CDR1 domain comprising the amino acid sequence of SEQ ID NO: 8, and 
 
 (c) an isolated human antibody comprising a light chain variable region (LCVR) comprising the amino acid sequence of SEQ ID NO: 1 and a heavy chain variable region (HCVR) comprising the amino acid sequence of SEQ ID NO: 2. 
 
     
     
         41 - 42 . (canceled) 
     
     
         43 . The kit of  claim 34 , wherein the IBD is Crohn's disease or ulcerative colitis. 
     
     
         44 . The kit of  claim 34 , wherein the means for determining the level of expression of TNFα in the cells is a means for determining the level of membrane TNFα in the cells of the intestinal mucosa.